This is a limit of ext3, you can remove the empty directories, these just are working directory.
For "image-versioned "I think this bug is fix in 4.5 (or even 4.4). But more generally, this problem can happen if you have over 32K images in a node ...
The next big eZ in production environment, I will still install a Debian but over ReseirFS In the meantime, the workaround is something like that: